Paper Citing NAMD - Abstract
Wang, Cun Xin; Liu, Ming; Li, Ping; Cong, Xiao Jing; Tan, Jian Jun; Chen, Wei Zu
Study on the Binding Mode of the Integrase with DNA via Steered Molecular Dynamics Simulation
2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20, 4894-4897, 2009
Human immunodeficiency virus type I (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. In the current work, a model for the active site of IN and viral DNA was built by combining experimental data with the results of steered molecular dynamics simulation. The model was then taken into a series automatic molecular docking calculations with two groups of inhibitors. According to the results of molecular docking, the inhibitors of the second group share a similar binding model with those of the first group, though they have no common scaffold. The newly built model of the IN-DNA complex is helpful for our subsequent research on the design of IN inhibitors.
